Biotech-equipment maker Affymetrix ( AFFX) said today it would not come anywhere near Wall Street estimates for the second quarter, citing slower-than-expected sales.

The Santa Clara, Calif.-based company said it expects to post a net loss of $4 million to $7 million in the second quarter, excluding noncash charges.

Based on 57.6 million outstanding shares, that puts the company's loss at 6 cents a share to 12 cents a share. Wall Street was looking for a net loss of 1 cent a share, according to Multex.com.

Revenue for the quarter is expected to reach between $44 million and $50 million, the company said today, compared with Wall Street's estimate of $58.1 million.

Shares in Affymetrix, which makes gene chips used in the drug discovery process, fell $3.76, or 8.4%, to $40.95 in Monday trading. The second-quarter warning was released after the market's close.

In its statement, the company blamed the shortfall on lower-than-anticipated orders for its GeneChip product line and a further decline in the sales of spotted array instruments, mainly to large pharmaceutical customers. The company said it is taking unspecified steps to manage expenses but is not ratcheting down research and development investments to avoid harming its long-term business prospects.

And Affymetrix's visibility is spotty, at best. The slowing economy is "contributing to the unanticipated weakness in orders, making it increasingly difficult for the company to predict its financial performance with certainty at this time," the company said in its statement, adding that a sales slowdown could last for the next two or three quarters.

This is the second-straight quarter of disappointing news from Affymetrix. The company reported a first-quarter net loss of 11 cents a share, missing Wall Street estimates by 7 cents. The company blamed the miss on the recall of one its chip products due to a design error.